During an event on Thursday in Cambridge, Mass., Crowley called the treatment of Manning, whom military jailers forced to sleep naked for several days last week, "ridiculous and counterproductive and stupid."

Asked about Crowley's remarks at a news conference Friday, President Obama said he "asked the Pentagon whether or not the procedures that have been taken in terms of his confinement are appropriate and are meeting our basic standards. They assured me that they are."

Crowley confirmed in a statement on Sunday that he has submitted his resignation and "takes full responsibility" for his statements. He also said that "The exercise of power in today's challenging times and relentless media environment must be prudent and consistent with our laws and values."

Clinton said in a statement that she accepted Crowley's resignation "with regret" and praised his "deep devotion to public policy and public diplomacy." Former National Security Council spokesman Mike Hammer, who recently transitioned to the State Department, will replace Crowley.